FLASHHelperClasses.h File Reference

#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
#include <boost/dynamic_bitset.hpp>

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Classes
struct	FLASHHelperClasses
	Wrapper struct for all the structs needed by the FLASHDeconv Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) TopPicItem - represent TopPic identification. Currently used for setQscore training. TopPic is the top-down proteomics identification tool (https://www.toppic.org/). iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. More...
class	FLASHHelperClasses::PrecalculatedAveragine
	Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation. More...
struct	FLASHHelperClasses::MassFeature
	Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features). More...
struct	FLASHHelperClasses::IsobaricQuantities
	Isobaric quantities. More...
class	FLASHHelperClasses::LogMzPeak
	log transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored. More...
class	FLASHHelperClasses::Tag
	Sequence tag. No mass gap is allowed in the seq. The mass gap containing tag should be enumerated into multiple Tag instances from outside. More...
class	FLASHHelperClasses::DAG

Namespaces
	OpenMS
	FLASHIda C++ to C# (or vice versa) bridge functions The functions here are called in C# to invoke functions in FLASHIda class.